Metrics, QC & all pipeline in longitudinal space (Stage 6 of #301)#317
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Implement rbc longitudinal metrics: resolve per-regressor regressed_bold/cleaned_bold + brain mask from space-longitudinal functional derivatives, read TR from NIfTI header, and call single_session_metrics unchanged. Reuse cross-sectional export_metrics for BIDS output naming. Co-authored-by: Janhavi Pillai <janhavipillai3@gmail.com>
QC: Dice/Jaccard overlap between anatomical and BOLD brain masks in longitudinal space with pass/fail threshold (Dice >= 0.85). Minimal scope per plan; viz tracked in #303/#304. All: rbc longitudinal all chains template -> anat -> func -> metrics -> qc. Template writes to disk (cross-session), then per-session stages pass func outputs in-memory to metrics and QC. CLI: Add --regressor and --task to rbc longitudinal all. Update descriptions for metrics/qc (no longer placeholders). Update unit tests to match (dispatch tests use mocks instead of NotImplementedError). Tests: Tier-4 full_pipeline tests for longitudinal metrics, QC, and the all-vs-sequential equivalence test under tests/full_pipeline/longitudinal/. process_anat/process_func now return their workflow outputs for in-memory handoff.
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The T1w suffix filter in run() excluded mask files from the DataFrame passed to process_anat, so resolve_longitudinal_anat could never find the brain mask. Remove the filter so both T1w and mask rows are grouped together. Pre-existing bug from Stage 4 exposed by the new full_pipeline tests.
Replace fragile DataFrame-based regressor discovery (which queried a non-existent 'reg' column) with an explicit --regressor parameter, matching the cross-sectional metrics CLI pattern.
The all fixture ran cross-sectional functional only for ses-test but invoked rbc longitudinal all without --session-label, causing it to iterate ses-retest (which has no functional derivatives) and crash on an empty BOLD DataFrame.
Template generation needs all sessions to find multi-session subjects. The session/task filters should only apply to per-session stages (anat, func, metrics, qc), not to discover_template_inputs which requires the full cross-session view.
TR handling: - Promote resolve_tr/warn_implausible_tr to public API in metadata.py - Replace bare _read_header_tr with _read_derivative_tr that pipes through resolve_tr for validation and plausibility warnings - Add --tr override to rbc longitudinal metrics CLI, matching cross-sectional FreeSurfer auth: - Rename _setup_freesurfer_auth -> setup_freesurfer_auth and add to __all__ in template.py - Import at module level in all.py instead of lazy private import QC DataFrame assembly: - Replace manual concat of session.anat + session.func + tpl_df with load_table call, matching cross-sectional qc.py pattern
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Summary
rbc longitudinal metricsresolves per-regressorregressed_bold/cleaned_bold+ brain mask fromspace-longitudinalfunctional derivatives, reads TR from the NIfTI header, and callssingle_session_metricsunchanged. Reuses cross-sectionalexport_metricsfor BIDS output naming (ALFF, fALFF, ReHo, atlas timeseries/correlations). CLI mirrors cross-sectional with--atlas(default schaefer_200) and--fwhm(default 6.0).rbc longitudinal qccomputes Dice/Jaccard overlap between the anatomical brain mask and BOLD brain mask in longitudinal template space. Pass/fail threshold at Dice >= 0.85. Minimal scope per plan; no visualizations (tracked in Cross-sectional QC visualization pipeline #303/Longitudinal QC visualization pipeline #304).rbc longitudinal allchains template -> anat -> func -> metrics -> qc. Template step writes to disk (cross-session), then per-session stages pass functional outputs in-memory to metrics and QC. CLI gains--regressorand--taskflags.process_anat/process_funcnow return their workflow outputs (AnatomicalLongOutputs/FunctionalLongOutputs) for in-memory handoff.full_pipelinetests for metrics, QC, and the all-vs-sequential equivalence test undertests/full_pipeline/longitudinal/. Unit test dispatch tests updated fromNotImplementedErrorchecks to mock-based routing verification.Ports metrics work from closed #297.
Closes the Stage 6 checkbox on #301.
Test plan
uv run ruff checkpasses on all changed filesuv run mypypasses on all changed modulesuv run pytest -m unitpasses (780 passed)uv run pytest -m integration --runner docker(nightly lane)uv run pytest -m full_pipeline --runner dockerfortests/full_pipeline/longitudinal/(release lane)